Gymnocalycium esperanzae Řepka and Kulhânek, has been recently described from the north central part of Argentina. In this paper the phylogenetic position and hybrid origin of this taxon are explored. Plant material of the supposed parental species was included in phylogenetic analyses with other members of three subgenera of the genus. The results of molecular analyses (cpDNA markers trnL-F, matK and AFLP) showed that G. esperanzae is closely related to members of the subgenus Trichomosemineum, especially G. bodenbenderianum and G. quehlianum. The second supposed parental species, G. castellanosii subsp. armillatum, was separated on a different branch in the tree. According to the special features of its seeds, which are similar to those of G. castellanosii, it clearly belongs to the subgenus Scabrosemineum. Also, molecular data were compared with morphological characters of its supposed parental species: G. bodenbenderianum (subgenus Trichomosemineum) and G. castellanosii subsp. armillatum (subgenus Scabrosemineum), which both grow near the locality of G. esperanzae. G. esperanzae has a very particular set of morphological features, some unique, others intermediate or more inclined to G. bodenbenderianum. Chloroplast DNA sequence analysis and AFLP analysis in combination with morphological features of all three species reveal a hypothesis of a hybrid origin of G. esperanzae.